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The Li Lab High-Performance Computing Cluster (“Genome) and Bioinformatics Toolsets

 

The Li lab High Performance Computing (HPC) Cluster (“Genome”) provides an environment for the processing, and bioinformatic, and statistical analyses of genomic, transcriptomic, epigenomic, and proteomic data.

The Cluster (“Genome”) currently consists of a head node (“Nucleus”), 17 compute nodes (“Chr1-17”), and a scratch storage node (“Mito”). This Cluster currently has 92 TB total combined storage space. Each of the compute nodes has 48 GB RAM and 8 physical (16 logical) cores.

An extensive array of software has been installed on the cluster to allow for processing of a wide variety of omics data types. Installed packages include R, Perl, Python, Slurm, BWA, SAMTools, GATK, Bowtie, Annovar, SNPEff, PLINK, VirusFinder2, VAAST/pVAAST, Consed, BLAST, Variant Tools, SOLAR, MERLIN, and many others. 

 

1. Hardware

2. Operating system

3. Installed General Software

4. Complete List of Installed Software for Genetics, Genomics, and Bioinformatics Research

5. How do I get an account?

6. Logging in

7. Software Locations

8. Submitting jobs

            8.1. Main Slurm Commands

9. Installing Software

      9.1. Perl Packages

9.2. Python Packages

9.3. R Packages

9.4. Local Installation

9.5 Installation Tips

10 Links

 

1. Hardware

-          1 x Head Node

o   8 GB RAM

o   3.7 GHz AMD A4-6300 Dual Core Processor

o   36 TB Storage

  5 TB System Drive

  28 TB RAID10 Home

  3 TB RAID10 Program Space

 

-          1 x Scratch Node

o   8 GB RAM

o   3.7 GHz AMD A4-6300 Dual Core Processor

o   32 TB Storage

  2 TB System Drive

  30 TB RAID5+0 Scratch Space

 

-          17 x Compute Node

o   HP ProLiant DL360 G6

o   48 GB RAM

o   Dual 2.93 GHz x5570 Quad Core Processor

o   72 GB Local Disk

 

2. Operating system

-          Head and Compute nodes are running Scientific Linux 7.3 (https://www.scientificlinux.org/ built on CentOS 7.3) and have been configured with OpenHPC 1.3 (https://openhpc.community/). Compute node image provisioning/management implemented via Warewulf 3.6 as part of OpenHPC (http://warewulf.lbl.gov/trac)

 

3. Installed General Software

-          Programming Languages

o   Java JDK 1.8.0_131

o   Python 3.6.1 (default)

o   Python 2.7.13

o   R 3.4.0

o   Perl 5.25.12-thread-multi-ld (default)

o   Perl 5.25.12-thread-multi

o   Perl 5.25.12-ld

o   Perl 5.25.12

o   Perl 5.16.3-thread-multi-ld

o   Perl 5.16.3-thread-multi

o   Perl 5.16.3-ld

o   Perl 5.16.3

 

-          Compilers/Compilation tools

o   gcc 5.4.0

o   LLVM 4.0

o   cmake 3.8.0

o   gmake 3.82

o   ant 1.10.0

 

-          Batch Scheduler

o   Slurm 16.05.9

 

-          Monitoring/Performance Tools

o   Nagios 4.3.1

o   Ganglia 3.7.2

o   Bmon 3.6

 

4. Complete Software Listing

-          More than 250 software packages/toolsets have been installed on the cluster. These include tools for (alphabetic order) Sequencing Alignment, Annotation, Assembly, Association, BS Seq, CHiP Seq, CLIP Seq, CNV, Data Format Manipulation, De Novo Assembly, HiC, IBD, Image Analysis, Imputation, Informatics, Liftover, Local Alignment, Low Complexity, Motif, ORF, Pedigree, Phasing, Programming Languages/Libraries, QC, QTL, Repeats, RNA Seq, Simulation, SV, Variant Detection, Viral Integration, and Visualization.

 

-          A full list of software can be downloaded here.

 

5. How do I get an account?

-          To obtain access to the Li lab cluster (genome), please contact Dawei Li:

 

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The rest of the manual is currently only open to registered users.

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